## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=999 INPUT=[/ceph/rimlsfnwi/data/moldevbio/zhou/jsmits/Ananse_test_data/RNAseq/results/star/hg38-PRIM_RNA_2.samtools-coordinate-sieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/zhou/jsmits/Ananse_test_data/RNAseq/results/final_bam/hg38-PRIM_RNA_2.samtools-coordinate.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/zhou/jsmits/Ananse_test_data/RNAseq/results/qc/markdup/hg38-PRIM_RNA_2.samtools-coordinate.metrics.txt REMOVE_DUPLICATES=true TMP_DIR=[/scratch/jsmits/tmp/aa5P]    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
## htsjdk.samtools.metrics.StringHeader
# Started on: Fri Feb 12 14:31:33 CET 2021

## METRICS CLASS	picard.sam.DuplicationMetrics
LIBRARY	UNPAIRED_READS_EXAMINED	READ_PAIRS_EXAMINED	SECONDARY_OR_SUPPLEMENTARY_RDS	UNMAPPED_READS	UNPAIRED_READ_DUPLICATES	READ_PAIR_DUPLICATES	READ_PAIR_OPTICAL_DUPLICATES	PERCENT_DUPLICATION	ESTIMATED_LIBRARY_SIZE
Unknown Library	246	11810723	0	0	178	2327050	2947	0.197034	25914456

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.000197	8763309	0	8765543
2.0	1.634289	494183	2884	492199
3.0	2.036283	99660	10	99471
4.0	2.291133	41327	1	41304
5.0	2.4527	22334	3	22323
6.0	2.555129	13406	0	13398
7.0	2.620065	8781	2	8775
8.0	2.661232	6302	1	6302
9.0	2.687331	4725	0	4717
10.0	2.703877	3589	1	3593
11.0	2.714366	2752	0	2751
12.0	2.721016	2122	0	2116
13.0	2.725232	1810	0	1811
14.0	2.727905	1527	0	1525
15.0	2.729599	1252	0	1256
16.0	2.730673	1103	0	1102
17.0	2.731354	904	0	904
18.0	2.731786	846	0	843
19.0	2.73206	708	0	713
20.0	2.732233	627	0	624
21.0	2.732343	582	0	583
22.0	2.732413	510	0	507
23.0	2.732457	479	0	481
24.0	2.732485	435	0	435
25.0	2.732503	398	0	396
26.0	2.732514	339	0	339
27.0	2.732521	311	0	313
28.0	2.732526	288	0	286
29.0	2.732529	276	0	278
30.0	2.732531	280	0	278
31.0	2.732532	246	0	246
32.0	2.732532	234	0	234
33.0	2.732533	176	0	177
34.0	2.732533	211	0	209
35.0	2.732533	171	0	174
36.0	2.732533	169	0	167
37.0	2.732534	155	0	154
38.0	2.732534	154	0	158
39.0	2.732534	154	0	155
40.0	2.732534	139	0	136
41.0	2.732534	125	0	124
42.0	2.732534	99	0	100
43.0	2.732534	125	0	125
44.0	2.732534	122	0	122
45.0	2.732534	112	0	110
46.0	2.732534	108	0	110
47.0	2.732534	98	0	97
48.0	2.732534	94	0	95
49.0	2.732534	80	0	78
50.0	2.732534	77	0	78
51.0	2.732534	94	0	93
52.0	2.732534	92	0	92
53.0	2.732534	73	0	74
54.0	2.732534	70	0	69
55.0	2.732534	77	0	78
56.0	2.732534	52	0	51
57.0	2.732534	58	0	60
58.0	2.732534	71	0	69
59.0	2.732534	57	0	59
60.0	2.732534	55	0	53
61.0	2.732534	53	0	53
62.0	2.732534	60	0	60
63.0	2.732534	48	0	49
64.0	2.732534	42	0	41
65.0	2.732534	48	0	50
66.0	2.732534	57	0	55
67.0	2.732534	60	0	60
68.0	2.732534	49	0	49
69.0	2.732534	55	0	55
70.0	2.732534	36	0	37
71.0	2.732534	42	0	41
72.0	2.732534	38	0	39
73.0	2.732534	45	0	44
74.0	2.732534	38	0	38
75.0	2.732534	45	0	45
76.0	2.732534	28	0	28
77.0	2.732534	36	0	36
78.0	2.732534	39	0	41
79.0	2.732534	36	0	34
80.0	2.732534	26	0	27
81.0	2.732534	30	0	30
82.0	2.732534	37	0	36
83.0	2.732534	27	0	27
84.0	2.732534	32	0	32
85.0	2.732534	19	0	20
86.0	2.732534	22	0	23
87.0	2.732534	26	0	25
88.0	2.732534	27	0	27
89.0	2.732534	28	0	27
90.0	2.732534	27	0	27
91.0	2.732534	25	0	26
92.0	2.732534	35	0	34
93.0	2.732534	20	0	20
94.0	2.732534	20	0	20
95.0	2.732534	23	0	24
96.0	2.732534	19	0	18
97.0	2.732534	23	0	23
98.0	2.732534	12	0	13
99.0	2.732534	27	0	27
100.0	2.732534	17	0	16
101.0	0	20	0	21
102.0	0	23	0	22
103.0	0	17	0	21
104.0	0	13	0	9
105.0	0	21	0	21
106.0	0	24	0	25
107.0	0	19	0	18
108.0	0	18	0	19
109.0	0	18	0	17
110.0	0	13	0	13
111.0	0	17	0	17
112.0	0	9	0	10
113.0	0	14	0	14
114.0	0	12	0	11
115.0	0	13	0	13
116.0	0	13	0	14
117.0	0	16	0	15
118.0	0	19	0	19
119.0	0	12	0	13
120.0	0	13	0	13
121.0	0	12	0	11
122.0	0	12	0	13
123.0	0	19	0	18
124.0	0	14	0	14
125.0	0	14	0	14
126.0	0	7	0	7
127.0	0	6	0	6
128.0	0	19	0	19
129.0	0	17	0	17
130.0	0	13	0	13
131.0	0	9	0	10
132.0	0	14	0	13
133.0	0	16	0	16
134.0	0	18	0	18
135.0	0	4	0	4
136.0	0	14	0	14
137.0	0	13	0	13
138.0	0	13	0	13
139.0	0	10	0	10
140.0	0	5	0	5
141.0	0	11	0	11
142.0	0	9	0	9
143.0	0	9	0	9
144.0	0	7	0	7
145.0	0	10	0	10
146.0	0	7	0	7
147.0	0	7	0	7
148.0	0	12	0	12
149.0	0	7	0	7
150.0	0	7	0	7
151.0	0	6	0	6
152.0	0	14	0	14
153.0	0	12	0	13
154.0	0	9	0	8
155.0	0	11	0	12
156.0	0	10	0	9
157.0	0	8	0	8
158.0	0	12	0	12
159.0	0	8	0	8
160.0	0	10	0	10
161.0	0	6	0	8
162.0	0	5	0	3
163.0	0	10	0	10
164.0	0	6	0	6
165.0	0	9	0	9
166.0	0	3	0	3
167.0	0	4	0	4
168.0	0	8	0	8
169.0	0	12	0	13
170.0	0	8	0	7
171.0	0	13	0	13
172.0	0	14	0	14
173.0	0	5	0	5
174.0	0	6	0	6
175.0	0	9	0	9
176.0	0	9	0	9
177.0	0	9	0	9
178.0	0	5	0	6
179.0	0	8	0	8
180.0	0	6	0	6
181.0	0	7	0	6
182.0	0	4	0	4
183.0	0	5	0	5
184.0	0	8	0	8
185.0	0	6	0	6
186.0	0	5	0	5
187.0	0	9	0	9
188.0	0	7	0	7
189.0	0	7	0	7
190.0	0	3	0	3
191.0	0	7	0	7
192.0	0	4	0	5
193.0	0	4	0	3
194.0	0	8	0	9
195.0	0	10	0	9
196.0	0	6	0	6
197.0	0	7	0	7
198.0	0	4	0	4
199.0	0	7	0	7
200.0	0	3	0	3
201.0	0	5	0	5
202.0	0	3	0	3
203.0	0	4	0	4
204.0	0	2	0	2
205.0	0	1	0	1
206.0	0	6	0	6
207.0	0	6	0	6
208.0	0	5	0	5
209.0	0	6	0	6
210.0	0	10	0	10
211.0	0	6	0	6
212.0	0	4	0	4
213.0	0	10	0	11
214.0	0	7	0	7
215.0	0	2	0	2
216.0	0	4	0	3
217.0	0	8	0	8
218.0	0	5	0	5
219.0	0	4	0	4
220.0	0	4	0	6
221.0	0	6	0	4
222.0	0	4	0	4
223.0	0	6	0	6
224.0	0	2	0	2
225.0	0	4	0	4
226.0	0	4	0	4
227.0	0	4	0	4
228.0	0	5	0	5
229.0	0	3	0	3
230.0	0	1	0	1
231.0	0	3	0	3
232.0	0	5	0	5
233.0	0	4	0	5
234.0	0	3	0	2
235.0	0	4	0	4
236.0	0	4	0	4
237.0	0	2	0	2
238.0	0	3	0	3
239.0	0	4	0	4
240.0	0	4	0	4
241.0	0	6	0	6
242.0	0	1	0	1
243.0	0	0	0	1
244.0	0	9	0	8
245.0	0	6	0	6
246.0	0	1	0	1
247.0	0	1	0	1
248.0	0	4	0	4
249.0	0	4	0	5
250.0	0	3	0	3
251.0	0	6	0	5
252.0	0	6	0	6
253.0	0	2	0	3
254.0	0	6	0	5
255.0	0	1	0	1
256.0	0	1	0	1
257.0	0	5	0	5
258.0	0	1	0	1
259.0	0	10	0	10
260.0	0	3	0	3
261.0	0	4	0	4
262.0	0	3	0	3
263.0	0	4	0	4
264.0	0	2	0	2
265.0	0	3	0	3
266.0	0	4	0	4
267.0	0	0	0	1
268.0	0	5	0	4
269.0	0	1	0	1
270.0	0	3	0	3
271.0	0	2	0	2
272.0	0	2	0	2
273.0	0	3	0	3
274.0	0	3	0	3
275.0	0	3	0	3
276.0	0	4	0	4
277.0	0	3	0	3
278.0	0	2	0	2
279.0	0	1	0	1
280.0	0	3	0	3
281.0	0	2	0	3
282.0	0	4	0	3
284.0	0	1	0	1
285.0	0	2	0	2
286.0	0	3	0	3
287.0	0	5	0	5
288.0	0	1	0	1
289.0	0	1	0	1
291.0	0	4	0	4
292.0	0	2	0	2
293.0	0	1	0	2
294.0	0	2	0	1
295.0	0	3	0	3
296.0	0	0	0	1
297.0	0	2	0	1
298.0	0	2	0	2
299.0	0	1	0	1
300.0	0	2	0	2
301.0	0	1	0	1
302.0	0	2	0	3
303.0	0	3	0	2
304.0	0	1	0	1
305.0	0	2	0	2
307.0	0	1	0	1
308.0	0	2	0	2
309.0	0	5	0	5
310.0	0	0	0	1
311.0	0	5	0	4
312.0	0	3	0	3
313.0	0	1	0	1
314.0	0	1	0	1
315.0	0	2	0	2
316.0	0	1	0	1
317.0	0	3	0	3
318.0	0	2	0	2
319.0	0	3	0	3
320.0	0	1	0	1
321.0	0	2	0	2
322.0	0	2	0	2
323.0	0	2	0	2
324.0	0	1	0	1
325.0	0	1	0	1
326.0	0	4	0	4
327.0	0	2	0	2
328.0	0	6	0	7
329.0	0	2	0	1
330.0	0	3	0	3
331.0	0	3	0	3
332.0	0	1	0	1
333.0	0	2	0	2
334.0	0	1	0	1
336.0	0	1	0	1
338.0	0	4	0	4
339.0	0	1	0	1
340.0	0	2	0	2
341.0	0	2	0	2
342.0	0	1	0	1
343.0	0	2	0	2
344.0	0	1	0	1
345.0	0	1	0	1
346.0	0	1	0	1
347.0	0	2	0	2
349.0	0	1	0	1
351.0	0	2	0	2
352.0	0	1	0	1
353.0	0	2	0	3
354.0	0	3	0	2
355.0	0	3	0	3
356.0	0	1	0	1
357.0	0	3	0	3
358.0	0	1	0	1
359.0	0	2	0	2
360.0	0	5	0	5
361.0	0	1	0	1
363.0	0	2	0	2
364.0	0	2	0	2
365.0	0	2	0	2
366.0	0	1	0	1
370.0	0	1	0	1
371.0	0	3	0	3
372.0	0	3	0	3
373.0	0	1	0	3
374.0	0	3	0	1
375.0	0	1	0	1
376.0	0	2	0	2
377.0	0	2	0	2
379.0	0	2	0	2
382.0	0	1	0	1
384.0	0	2	0	3
385.0	0	2	0	1
386.0	0	0	0	1
387.0	0	1	0	1
388.0	0	2	0	1
389.0	0	2	0	2
390.0	0	1	0	2
391.0	0	4	0	3
393.0	0	2	0	2
394.0	0	0	0	1
395.0	0	2	0	1
397.0	0	2	0	2
398.0	0	1	0	3
399.0	0	4	0	2
400.0	0	2	0	2
401.0	0	1	0	1
402.0	0	2	0	2
403.0	0	0	0	1
404.0	0	3	0	3
405.0	0	1	0	1
406.0	0	2	0	1
407.0	0	0	0	1
408.0	0	3	0	2
409.0	0	2	0	2
410.0	0	1	0	1
411.0	0	1	0	1
412.0	0	1	0	1
414.0	0	1	0	1
415.0	0	2	0	2
416.0	0	3	0	3
419.0	0	1	0	1
420.0	0	2	0	2
421.0	0	1	0	1
423.0	0	2	0	2
424.0	0	2	0	3
425.0	0	2	0	1
427.0	0	2	0	2
428.0	0	3	0	3
429.0	0	1	0	1
432.0	0	0	0	1
433.0	0	2	0	1
434.0	0	1	0	1
436.0	0	1	0	1
439.0	0	1	0	1
440.0	0	1	0	1
442.0	0	1	0	1
443.0	0	1	0	1
444.0	0	2	0	2
445.0	0	3	0	3
446.0	0	1	0	2
447.0	0	1	0	0
448.0	0	2	0	2
449.0	0	1	0	1
454.0	0	2	0	2
456.0	0	1	0	1
459.0	0	1	0	1
461.0	0	1	0	1
462.0	0	1	0	1
467.0	0	1	0	1
468.0	0	1	0	1
469.0	0	1	0	1
471.0	0	1	0	1
474.0	0	1	0	1
477.0	0	1	0	2
478.0	0	1	0	0
479.0	0	1	0	1
480.0	0	3	0	3
483.0	0	1	0	1
485.0	0	1	0	1
486.0	0	1	0	1
487.0	0	1	0	1
488.0	0	1	0	2
489.0	0	1	0	0
491.0	0	1	0	1
492.0	0	1	0	1
493.0	0	2	0	2
494.0	0	1	0	1
497.0	0	3	0	3
498.0	0	1	0	1
499.0	0	1	0	2
500.0	0	1	0	0
502.0	0	1	0	1
503.0	0	1	0	1
504.0	0	1	0	1
505.0	0	1	0	1
506.0	0	2	0	2
508.0	0	2	0	2
511.0	0	1	0	1
513.0	0	0	0	1
514.0	0	1	0	0
516.0	0	1	0	1
517.0	0	2	0	2
518.0	0	1	0	1
521.0	0	2	0	2
523.0	0	1	0	1
526.0	0	2	0	2
528.0	0	0	0	1
529.0	0	1	0	1
530.0	0	2	0	1
534.0	0	1	0	1
535.0	0	1	0	1
538.0	0	1	0	1
541.0	0	1	0	1
543.0	0	2	0	2
544.0	0	1	0	1
546.0	0	1	0	1
547.0	0	1	0	2
548.0	0	2	0	1
550.0	0	1	0	1
553.0	0	1	0	1
555.0	0	1	0	1
556.0	0	0	0	1
557.0	0	2	0	1
558.0	0	3	0	3
560.0	0	1	0	1
561.0	0	1	0	1
568.0	0	1	0	1
569.0	0	3	0	3
573.0	0	1	0	2
574.0	0	1	0	0
581.0	0	1	0	1
585.0	0	3	0	3
586.0	0	1	0	1
587.0	0	1	0	2
588.0	0	3	0	2
599.0	0	1	0	1
603.0	0	0	0	2
604.0	0	2	0	0
605.0	0	1	0	1
607.0	0	1	0	1
610.0	0	1	0	1
611.0	0	1	0	1
612.0	0	1	0	1
616.0	0	1	0	1
619.0	0	1	0	1
626.0	0	1	0	2
627.0	0	1	0	0
629.0	0	1	0	1
631.0	0	1	0	1
632.0	0	1	0	1
635.0	0	1	0	1
637.0	0	2	0	2
639.0	0	1	0	1
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648.0	0	1	0	1
653.0	0	1	0	1
657.0	0	1	0	1
661.0	0	1	0	1
664.0	0	1	0	1
671.0	0	3	0	3
674.0	0	1	0	1
675.0	0	1	0	1
679.0	0	0	0	1
680.0	0	2	0	1
681.0	0	1	0	1
682.0	0	1	0	1
692.0	0	1	0	1
695.0	0	2	0	2
698.0	0	1	0	1
700.0	0	1	0	2
701.0	0	1	0	0
702.0	0	1	0	1
704.0	0	1	0	1
714.0	0	0	0	1
715.0	0	1	0	0
716.0	0	1	0	1
717.0	0	1	0	1
718.0	0	1	0	1
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